Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001413.1 Hibiscus syriacus cultivar Beakdansim tig00002750_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 112515
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:3768 original size:21 final size:21
Alignment explanation
Indices: 3742--3782 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3732 TATGATATGA
*
3742 ACAGTAACCTGCTATAGTACT
1 ACAGTAACCTGCTACAGTACT
3763 ACAGTAACCTGCTACAGTAC
1 ACAGTAACCTGCTACAGTAC
3783 AATGCATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (21 bp):
ACAGTAACCTGCTACAGTACT
Found at i:3881 original size:21 final size:21
Alignment explanation
Indices: 3838--3881 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3828 AATGGCAATT
*
3838 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGATACA
*
3859 GTGCATCGATGCACTGATGCA
1 GTGCATCGATGCACTGATACA
3880 GT
1 GT
3882 ACTGTTACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACTGATACA
Found at i:7278 original size:21 final size:21
Alignment explanation
Indices: 7254--7293 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7244 CCAATAGAGG
* *
7254 TTAATTATTTTTCAATTTTTA
1 TTAATCATTTTTAAATTTTTA
7275 TTAATCATTTTTAAATTTT
1 TTAATCATTTTTAAATTTT
7294 ACCTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAATCATTTTTAAATTTTTA
Found at i:7695 original size:21 final size:23
Alignment explanation
Indices: 7669--7714 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
7659 AATGAAAGTG
*
7669 TTTTTTTAAGTTAAAGATTATTA
1 TTTTTATAAGTTAAAGATTATTA
*
7692 TTTTTCATAAGTTAGAGATTATT
1 TTTTT-ATAAGTTAAAGATTATT
7715 TGTTTTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (23 bp):
TTTTTATAAGTTAAAGATTATTA
Found at i:14026 original size:23 final size:23
Alignment explanation
Indices: 14000--14046 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
13990 AGTTTTTCTT
14000 CGATTGAGATACACTCTATGAGG
1 CGATTGAGATACACTCTATGAGG
* *
14023 CGATTGAGATGCAGTCTATGAGG
1 CGATTGAGATACACTCTATGAGG
14046 C
1 C
14047 ACTCGCTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (23 bp):
CGATTGAGATACACTCTATGAGG
Found at i:15578 original size:23 final size:23
Alignment explanation
Indices: 15544--15621 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
15534 AGAATATTAA
*
15544 CCGAAGTG-CCACATAGATTTGTC
1 CCGAA-TGACCACATAGAATTGTC
*
15567 CCGAATGACCACTTAGAATTGTC
1 CCGAATGACCACATAGAATTGTC
* *
15590 CCGAA-GACCAAATAGAATTATC
1 CCGAATGACCACATAGAATTGTC
15612 CCGAATGACC
1 CCGAATGACC
15622 GCGTTGAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 21 0.44
23 27 0.56
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (23 bp):
CCGAATGACCACATAGAATTGTC
Found at i:15605 original size:22 final size:23
Alignment explanation
Indices: 15556--15621 Score: 89
Period size: 22 Copynumber: 2.9 Consensus size: 23
15546 GAAGTGCCAC
* *
15556 ATAGATTTGTCCCGAATGACCAC
1 ATAGAATTGTCCCGAATGACCAA
*
15579 TTAGAATTGTCCCGAA-GACCAA
1 ATAGAATTGTCCCGAATGACCAA
*
15601 ATAGAATTATCCCGAATGACC
1 ATAGAATTGTCCCGAATGACC
15622 GCGTTGAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (23 bp):
ATAGAATTGTCCCGAATGACCAA
Found at i:15752 original size:15 final size:15
Alignment explanation
Indices: 15732--15816 Score: 82
Period size: 15 Copynumber: 5.7 Consensus size: 15
15722 AAGTATTATT
15732 TATTCACATAAAACA
1 TATTCACATAAAACA
* *
15747 TATTCACCTAGAACA
1 TATTCACATAAAACA
* *
15762 TTTTCACATAGAACA
1 TATTCACATAAAACA
*
15777 TTTTCA-AGTAAAACA
1 TATTCACA-TAAAACA
* **
15792 CATTCACATTTAACA
1 TATTCACATAAAACA
15807 TATTCACATA
1 TATTCACATA
15817 CTAATAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
14 1 0.02
15 55 0.96
16 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (15 bp):
TATTCACATAAAACA
Found at i:16664 original size:76 final size:76
Alignment explanation
Indices: 16557--16752 Score: 272
Period size: 76 Copynumber: 2.6 Consensus size: 76
16547 TGTACAAGGT
* * *
16557 GGGAATCGGTACCCCCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTC-GGAG-CA
1 GGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGG-GCCA
**
16619 AAACTGTTTAGGG
65 AAACCATTTA-GG
* *
16632 GGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCAAGCATTCTGGAAATCTCAGGGCCAA
1 GGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGGGCCAA
16697 AACCATTTAGG
66 AACCATTTAGG
*
16708 GGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
16753 ATCTGTAATT
Statistics
Matches: 108, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
75 15 0.14
76 58 0.54
77 35 0.32
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.23
Consensus pattern (76 bp):
GGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGGGCCAA
AACCATTTAGG
Found at i:16968 original size:28 final size:28
Alignment explanation
Indices: 16934--16987 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
16924 CATTTGGAAA
16934 ATCTTAAAATCCATTTAACTTAATTTGT
1 ATCTTAAAATCCATTTAACTTAATTTGT
16962 ATCTTAAAATCCATTTAACTTAATTT
1 ATCTTAAAATCCATTTAACTTAATTT
16988 TTTATATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (28 bp):
ATCTTAAAATCCATTTAACTTAATTTGT
Found at i:17323 original size:21 final size:20
Alignment explanation
Indices: 17296--17394 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
17286 AATCAGTTTC
17296 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
17317 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
17338 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
17358 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
17379 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
17395 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:17387 original size:20 final size:20
Alignment explanation
Indices: 17362--17591 Score: 223
Period size: 20 Copynumber: 11.4 Consensus size: 20
17352 GATTTTCCAG
* ** *
17362 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
17382 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
17402 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
17422 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
17442 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
17462 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
17482 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
17502 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
* * *
17523 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
17543 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
17563 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
17583 AATCACAAC
1 AATCGCAAC
17592 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 27, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 156 0.89
21 19 0.11
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:18323 original size:24 final size:24
Alignment explanation
Indices: 18284--18330 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18274 AAATTTGGTC
18284 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
18308 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
18331 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:18522 original size:12 final size:12
Alignment explanation
Indices: 18505--18529 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18495 ATATAATCCT
18505 GAAGAAGAAAAA
1 GAAGAAGAAAAA
18517 GAAGAAGAAAAA
1 GAAGAAGAAAAA
18529 G
1 G
18530 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:20933 original size:72 final size:72
Alignment explanation
Indices: 20824--20975 Score: 270
Period size: 72 Copynumber: 2.1 Consensus size: 72
20814 GCAATGAGAG
20824 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
20889 AAATGAA
66 AAATGAA
* *
20896 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
20960 GAAATGAA
65 GAAATGAA
20968 AATCGCAA
1 AATCGCAA
20976 CGAGAGAATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
72 76 0.99
73 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:20945 original size:53 final size:52
Alignment explanation
Indices: 20810--21014 Score: 267
Period size: 53 Copynumber: 3.9 Consensus size: 52
20800 CGGAAATTAC
* *
20810 AATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
20857 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
20915 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
*
20968 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGA
21015 TTCTCTCGTT
Statistics
Matches: 141, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
47 8 0.06
50 1 0.01
52 14 0.10
53 102 0.72
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:21084 original size:53 final size:52
Alignment explanation
Indices: 21004--21121 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 52
20994 GAAATGAAAA
21004 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTACGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTACGATTTTCATT
*
21057 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
21109 TCCGCATTGCGAT
1 T-CGCATTGCGAT
21122 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 18 0.29
53 45 0.71
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTACGATTTTCATT
Found at i:21129 original size:20 final size:19
Alignment explanation
Indices: 21023--21121 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
21013 GATTCTCTCG
21023 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
21043 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
21062 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
21076 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
21095 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
21115 TTGCGAT
1 TTGCGAT
21122 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 24 0.35
20 25 0.36
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:21247 original size:14 final size:14
Alignment explanation
Indices: 21228--21264 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
21218 CATCAATTAC
21228 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
21242 ACAAATCATCTTTT
1 ACAAATCAACTTTT
21256 ACAAATCAA
1 ACAAATCAA
21265 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:22774 original size:21 final size:21
Alignment explanation
Indices: 22744--22790 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
22734 CTCGAGGAAT
22744 GATA-GGGGGGCCTCTTCAAC
1 GATAGGGGGGGCCTCTTCAAC
22764 GATAGGGGGGGCCTCTTCAAC
1 GATAGGGGGGGCCTCTTCAAC
22785 GATAGG
1 GATAGG
22791 AGTGGACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.19
Consensus pattern (21 bp):
GATAGGGGGGGCCTCTTCAAC
Found at i:22800 original size:21 final size:21
Alignment explanation
Indices: 22744--22801 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
22734 CTCGAGGAAT
*
22744 GATAGG-GGGGCCTCTTCAAC
1 GATAGGAGGGGACTCTTCAAC
* *
22764 GATAGGGGGGGCCTCTTCAAC
1 GATAGGAGGGGACTCTTCAAC
*
22785 GATAGGAGTGGACTCTT
1 GATAGGAGGGGACTCTT
22802 GAGGGATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (21 bp):
GATAGGAGGGGACTCTTCAAC
Found at i:23251 original size:19 final size:19
Alignment explanation
Indices: 23209--23381 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
23199 TAGTTTACTT
* *
23209 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
23229 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
23248 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
23267 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
23286 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23305 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
23319 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
23338 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
23352 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAATGAAAA
*
23371 TCGCAATGCGA
1 TCGCAACGCGA
23382 TTTTGGTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 81 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:23322 original size:14 final size:14
Alignment explanation
Indices: 23303--23359 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
23293 GCGAAATGAA
*
23303 AATCGCAACGACAG
1 AATCGCAACGAAAG
23317 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
23334 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
23350 AATCGCAACG
1 AATCGCAACG
23360 CGAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:23330 original size:33 final size:33
Alignment explanation
Indices: 23284--23376 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
23274 GCGAAACCAA
23284 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
23317 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
23350 AATCGCAACGCGAAATAAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
23377 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:23373 original size:52 final size:52
Alignment explanation
Indices: 23243--23381 Score: 138
Period size: 52 Copynumber: 2.7 Consensus size: 52
23233 AACGCGAAAT
* * * *
23243 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACAAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * * **
23295 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAAC-A-AAAATCGCAATGCGAAACCAAAATCGCAACGA
*
23347 GAGAATCGCAACGCGAAATAAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACAAAAATCGCAATGCGA
23382 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
50 7 0.11
51 3 0.05
52 45 0.68
53 4 0.06
54 7 0.11
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACAAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:23410 original size:14 final size:14
Alignment explanation
Indices: 23388--23452 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
23378 GCGATTTTGG
*
23388 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
23402 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
23416 TTTCATTTCGCATTGCGAT
1 TTTC---TCG--TTGCGAT
* *
23435 TCTGTCGTTGCGAT
1 TTTCTCGTTGCGAT
23449 TTTC
1 TTTC
23453 ATTTCGCGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 26 0.63
16 3 0.07
17 3 0.07
19 9 0.22
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:23425 original size:33 final size:33
Alignment explanation
Indices: 23377--23470 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
23367 AAAATCGCAA
**
23377 TGCGATTTTGGTTTCGCGTTGCGATTTTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
* * *
23410 TGCGATTTTCATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
23443 TGCGATTTTCATTTCGCGTTGCGATTTT
1 TGCGATTTTCATTTCGCGTTGCGATTTT
23471 GGTTTCGCGT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTTTCTCGT
Found at i:23431 original size:19 final size:18
Alignment explanation
Indices: 23377--23489 Score: 98
Period size: 19 Copynumber: 6.5 Consensus size: 18
23367 AAAATCGCAA
*
23377 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-CTTTCGCGT
23396 TGCGATTTTC--T--CGT
1 TGCGATTTTCTTTCGCGT
*
23410 TGCGATTTTCATTTCGCAT
1 TGCGATTTTC-TTTCGCGT
*
23429 TGCGA--TTCTGT--CGT
1 TGCGATTTTCTTTCGCGT
23443 TGCGATTTTCATTTCGCGT
1 TGCGATTTTC-TTTCGCGT
*
23462 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-CTTTCGCGT
23481 TGCGATTTT
1 TGCGATTTT
23490 AAGTTTCGTG
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.26
16 6 0.08
17 6 0.08
19 45 0.58
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.48
Consensus pattern (18 bp):
TGCGATTTTCTTTCGCGT
Found at i:23497 original size:20 final size:19
Alignment explanation
Indices: 23377--23505 Score: 93
Period size: 19 Copynumber: 7.3 Consensus size: 19
23367 AAAATCGCAA
*
23377 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
23396 TGCGA---T--TTTCTCGT
1 TGCGATTTTAGTTTCGCGT
*
23410 TGCGATTTTCA-TTTCGCAT
1 TGCGATTTT-AGTTTCGCGT
*
23429 TGCGATTCT-G--T--CGT
1 TGCGATTTTAGTTTCGCGT
23443 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTT-AGTTTCGCGT
*
23462 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
23481 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-AGTTTCGCGT
23501 TGCGA
1 TGCGA
23506 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 9, Indels: 27
0.71 0.07 0.22
Matches are distributed among these distances:
14 22 0.25
16 2 0.02
17 2 0.02
19 48 0.55
20 13 0.15
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.47
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:23693 original size:17 final size:17
Alignment explanation
Indices: 23671--23703 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23661 AATACTATTT
23671 CACAGTGTTA-AAGAATA
1 CACAGT-TTAGAAGAATA
23688 CACAGTTTAGAAGAAT
1 CACAGTTTAGAAGAAT
23704 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
CACAGTTTAGAAGAATA
Found at i:25419 original size:20 final size:20
Alignment explanation
Indices: 25388--25451 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
25378 TTTTGGTTGA
25388 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
25408 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
25428 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
25449 AAT
1 AAT
25452 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:25440 original size:21 final size:21
Alignment explanation
Indices: 25386--25450 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
25376 TCTTTTGGTT
25386 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
25407 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
25427 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
25448 GAA
1 GAA
25451 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:25509 original size:19 final size:19
Alignment explanation
Indices: 25476--25584 Score: 84
Period size: 19 Copynumber: 5.8 Consensus size: 19
25466 AAAATCGCAA
**
25476 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
25495 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
25514 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
25528 TGCGATTTTCATTTTTCTCGT
1 TGCGATTTTCA--TTTCGCGT
** *
25549 TGCAGATAGTCATTTTCACGT
1 TGC-GATTTTCA-TTTCGCGT
25570 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
25585 TCTCGTTGCG
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 26 0.35
20 6 0.08
21 20 0.27
22 6 0.08
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:25547 original size:21 final size:21
Alignment explanation
Indices: 25522--25595 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
25512 GTTGCGATTC
25522 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
25543 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
25564 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
25585 TCTCGTTGCGA
1 TCTCGTTGCGA
25596 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:25717 original size:33 final size:33
Alignment explanation
Indices: 25675--25745 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
25665 GATACTAACT
*
25675 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
* *
25708 TGAAAATCGCAACGAGAGAATCGTAACACGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACACGAAA
25741 TGAAA
1 TGAAA
25746 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACACGAAA
Found at i:26128 original size:20 final size:20
Alignment explanation
Indices: 26103--26296 Score: 230
Period size: 20 Copynumber: 9.6 Consensus size: 20
26093 CTTTAAAAAT
26103 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
26123 CGCGTTGCGATTTTTACGTAT-
1 CGCGTTGCGA--TTTACGGATA
*
26144 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
26165 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
26185 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
26205 TGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
26225 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
26245 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
26265 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
26285 CGCGTTGCGATT
1 CGCGTTGCGATT
26297 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
20 131 0.87
21 3 0.02
22 16 0.11
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:28786 original size:23 final size:21
Alignment explanation
Indices: 28735--28776 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
28725 TCCCCTGTGG
28735 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
28758 GGGGGAATCGGTTCCCTCA
1 GGGGGAATCGGTTCCCTCA
28777 GGGAGGGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 3 0.16
23 13 0.68
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:32633 original size:22 final size:21
Alignment explanation
Indices: 32591--32630 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32581 GAGTTTGTTT
*
32591 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
32612 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
32631 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:34659 original size:75 final size:76
Alignment explanation
Indices: 34555--34751 Score: 290
Period size: 75 Copynumber: 2.6 Consensus size: 76
34545 GTTGTACAAG
* * *
34555 GGGGGAATCGGTACCCCCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-C
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
**
34618 AAAACTGTTTA
66 AAAACCATTTA
* *
34629 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
34694 AAAACCATTTA
66 AAAACCATTTA
* *
34705 GGGGGAATCGGTTCCTCCTAAGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCT-ATGGGGGGAATCGGTTCCCTCCGAGCA
34752 ATCTGTAATT
Statistics
Matches: 111, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
74 17 0.15
75 40 0.36
76 29 0.26
77 25 0.23
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
AAAACCATTTA
Found at i:34964 original size:28 final size:28
Alignment explanation
Indices: 34930--34985 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34920 CATTTGGAAA
34930 ATCTTAAAATCCATTTAACTTAATTTGT
1 ATCTTAAAATCCATTTAACTTAATTTGT
34958 ATCTTAAAATCCATTTAACTTAATTTGT
1 ATCTTAAAATCCATTTAACTTAATTTGT
34986 TATATCGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.04, T:0.46
Consensus pattern (28 bp):
ATCTTAAAATCCATTTAACTTAATTTGT
Found at i:37155 original size:3 final size:3
Alignment explanation
Indices: 37139--37240 Score: 54
Period size: 3 Copynumber: 34.0 Consensus size: 3
37129 TATAAAATAA
* * *
37139 TAT TA- TAT TA- TAT TAT TAT ATAT T-T AAT TAT TAA TAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
*
37181 TAT TA- TAT TAT ATAT ATAT ATAT ATAA TAT TAT TA- TAT TAT TAAT
1 TAT TAT TAT TAT -TAT -TAT -TAT -TAT TAT TAT TAT TAT TAT T-AT
* *
37226 TAT TAA TAA TAT TAT
1 TAT TAT TAT TAT TAT
37241 ATATACATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
2 11 0.13
3 52 0.63
4 20 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:37157 original size:8 final size:8
Alignment explanation
Indices: 37144--37242 Score: 88
Period size: 8 Copynumber: 13.0 Consensus size: 8
37134 AATAATATTA
37144 TATTATAT
1 TATTATAT
37152 TATTATA-
1 TATTATAT
37159 TATT-TAAT
1 TATTAT-AT
37167 TATTA-A-
1 TATTATAT
*
37173 TAATATAT
1 TATTATAT
37181 TATTATAT
1 TATTATAT
37189 TA-TATA-
1 TATTATAT
37195 TA-TATAT
1 TATTATAT
*
37202 ATATAATAT
1 -TATTATAT
37211 TATTATAT
1 TATTATAT
37219 TATTA-AT
1 TATTATAT
*
37226 TATTAATAA
1 TATT-ATAT
37235 TATTATAT
1 TATTATAT
37243 ATACATTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
6 11 0.15
7 17 0.23
8 38 0.51
9 9 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTATAT
Found at i:37180 original size:19 final size:20
Alignment explanation
Indices: 37134--37242 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 20
37124 TTAAATATAA
37134 AATAATATTATATT-A-TATT
1 AATAATA-TATATTAATTATT
*
37153 -ATTATATAT-TTAATTATT
1 AATAATATATATTAATTATT
37171 AATAATATATTATT-A-TATT
1 AATAATATA-TATTAATTATT
37190 ATATATATATATATATAA-TATT
1 A-ATA-ATATATAT-TAATTATT
*
37212 -ATTATAT-TATTAATTATT
1 AATAATATATATTAATTATT
37230 AATAATATTATAT
1 AATAATA-TATAT
37243 ATACATTTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
16 2 0.03
17 7 0.10
18 16 0.22
19 21 0.29
20 11 0.15
21 11 0.15
22 5 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATAATATATATTAATTATT
Found at i:37213 original size:30 final size:27
Alignment explanation
Indices: 37139--37245 Score: 110
Period size: 30 Copynumber: 3.7 Consensus size: 27
37129 TATAAAATAA
*
37139 TATTATATTATATTATTATA-TATTTAAT
1 TATTA-ATAATATTATTATATTA-TTAAT
37167 TATTAATAATATATTATTATATTA-TATAT
1 TATTAAT-A-ATATTATTATATTATTA-AT
37196 ATATATATATAATATTATTATATTATTAAT
1 -TAT-TA-ATAATATTATTATATTATTAAT
37226 TATTAATAATATTATATATA
1 TATTAATAATATTAT-TATA
37246 CATTTAAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 18
0.78 0.01 0.20
Matches are distributed among these distances:
27 12 0.17
28 13 0.19
29 16 0.23
30 21 0.30
31 5 0.07
32 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTAATAATATTATTATATTATTAAT
Found at i:37220 original size:49 final size:48
Alignment explanation
Indices: 37134--37245 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 48
37124 TTAAATATAA
37134 AATAATATTATAT-TATATTATTATATATTTAATTATTAATAATATATT
1 AATAATATTATATATATATTATTATATATTTAATTATTAATAAT-TATT
* * *
37182 -ATTATATTATATATATA-TA-TATATAATATTATTATATTATTAATTATT
1 AATAATATTATATATATATTATTATAT-AT-TTAAT-TATTAATAATTATT
37230 AATAATATTATATATA
1 AATAATATTATATATA
37246 CATTTAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
46 5 0.09
47 15 0.27
48 12 0.22
49 23 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (48 bp):
AATAATATTATATATATATTATTATATATTTAATTATTAATAATTATT
Found at i:42280 original size:24 final size:24
Alignment explanation
Indices: 42253--42302 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
42243 GTGATAAGTG
42253 TTATAATCTGTT-AATTTTAAAAAA
1 TTATAAT-TGTTAAATTTTAAAAAA
* *
42277 TTATTATTTTTAAAATTTTAAAAAA
1 TTATAATTGTT-AAATTTTAAAAAA
42302 T
1 T
42303 ATTTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 3 0.14
24 6 0.27
25 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATAATTGTTAAATTTTAAAAAA
Found at i:44186 original size:29 final size:29
Alignment explanation
Indices: 44101--44186 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
44091 AATTAGTCCT
* *
44101 TAAACTTTTAAACATTCTAA--TCATCCA
1 TAAACTTTTGAATATTCTAATTTCATCCA
* * * **
44128 TAAAC-TATGACCCTCTTCTAATTTGGTCCA
1 TAAACTTTTGA--ATATTCTAATTTCATCCA
44158 TAAACTTTTGAATATTCTAATTTCATCCA
1 TAAACTTTTGAATATTCTAATTTCATCCA
44187 AATATGTAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
26 3 0.07
27 5 0.12
28 6 0.14
29 14 0.33
30 10 0.24
31 4 0.10
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (29 bp):
TAAACTTTTGAATATTCTAATTTCATCCA
Found at i:48444 original size:18 final size:18
Alignment explanation
Indices: 48423--48458 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
48413 GAAAGAGGGT
48423 CGTTGAGGAGCCGAGGAC
1 CGTTGAGGAGCCGAGGAC
*
48441 CGTTGAGGTGCCGAGGAC
1 CGTTGAGGAGCCGAGGAC
48459 GGAGTACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.44, T:0.14
Consensus pattern (18 bp):
CGTTGAGGAGCCGAGGAC
Found at i:51273 original size:27 final size:30
Alignment explanation
Indices: 51233--51299 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 30
51223 GATGATGTAG
* *
51233 AGAAAAATGAAAAAGAAAA-AGAAATA-GA
1 AGAAAAAGGAAAAAGAAAAGAGAAAGAGGA
*
51261 AGAAGAAGGAAAAAGAAAAGAGAAAGAGGA
1 AGAAAAAGGAAAAAGAAAAGAGAAAGAGGA
51291 AGAAAAAGG
1 AGAAAAAGG
51300 GAAGATTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 17 0.52
29 6 0.18
30 10 0.30
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (30 bp):
AGAAAAAGGAAAAAGAAAAGAGAAAGAGGA
Found at i:51304 original size:23 final size:24
Alignment explanation
Indices: 51247--51298 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
51237 AAATGAAAAA
*
51247 GAAAAAG-AAATAG-AAGAAGAAG
1 GAAAAAGAAAAGAGAAAGAAGAAG
*
51269 GAAAAAGAAAAGAGAAAGAGGAA-
1 GAAAAAGAAAAGAGAAAGAAGAAG
51292 GAAAAAG
1 GAAAAAG
51299 GGAAGATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 7 0.27
23 12 0.46
24 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (24 bp):
GAAAAAGAAAAGAGAAAGAAGAAG
Found at i:58934 original size:56 final size:56
Alignment explanation
Indices: 58827--58938 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
58817 TTTTAAATTG
* * * * **
58827 GTCCTTAAACTTTTGAATATTCTAATTTCGTCCCTAAACTATGACTTTCATTCTAA
1 GTCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGACCCTCATTCTAA
*
58883 GTCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGTCCCTCATTCTAA
1 GTCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGACCCTCATTCTAA
58939 ATTGATTCCC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (56 bp):
GTCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGACCCTCATTCTAA
Found at i:70711 original size:35 final size:35
Alignment explanation
Indices: 70660--70726 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
70650 TTTTCGAATT
70660 TATAATTTAATAAATATATAA-TTATAAAATATTA
1 TATAATTTAATAAATATATAATTTATAAAATATTA
* * *
70694 TATAATTTTAATTAATATTTAATTTATTAAATA
1 TATAA-TTTAATAAATATATAATTTATAAAATA
70727 CTATGTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 5 0.18
35 14 0.50
36 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
TATAATTTAATAAATATATAATTTATAAAATATTA
Found at i:78666 original size:20 final size:22
Alignment explanation
Indices: 78641--78681 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
78631 GGATTTTATT
78641 AACAATC-GAGCA-TATGCTTC
1 AACAATCAGAGCATTATGCTTC
78661 AACAATCAGAGCATTATGCTT
1 AACAATCAGAGCATTATGCTT
78682 AGCCAAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (22 bp):
AACAATCAGAGCATTATGCTTC
Found at i:79708 original size:82 final size:81
Alignment explanation
Indices: 79564--79861 Score: 339
Period size: 82 Copynumber: 3.6 Consensus size: 81
79554 ATTATACAAT
* * *
79564 TAAAAACCCAAGTTTATGATAAAGGATAGTTCAGATTTTGCTCAATAACTGCAAAATGAACTCTG
1 TAAAAAACCAAGTTTATGA-AAAGGGTAGTTCAGATTTTGCTCAAGAACTGCAAAATGAACTCTG
**
79629 AAATGA-TAGAACCCTT-
65 AAATGATTA-AACAATTA
* * * *
79645 TCGAAAAACCAAGTTTATGAAATAGGGTAGTTCAGATTTGGCTCAAGAACAGCAAAATGAACTCC
1 T-AAAAAACCAAGTTTATGAAA-AGGGTAGTTCAGATTTTGCTCAAGAACTGCAAAATGAACTCT
* *
79710 GAAACGATTAAATAATTA
64 GAAATGATTAAACAATTA
* *
79728 TAAAAAACCAAGTTTACGAAAAAGGGTAGTTCAGATTTTGCTCAAGAACTGCAAAATGAACCCTG
1 TAAAAAACCAAGTTTATG-AAAAGGGTAGTTCAGATTTTGCTCAAGAACTGCAAAATGAACTCTG
* *
79793 AAATAATAAAACAATTA
65 AAATGATTAAACAATTA
* * **
79810 TTAAAAAAACCAAGTTCATAAAAAGGGGTCCTTCAGATTTTGCTCAAGAACT
1 -T-AAAAAACCAAGTTTATGAAAA-GGGTAGTTCAGATTTTGCTCAAGAACT
79862 ACCGGAGTGA
Statistics
Matches: 183, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
81 3 0.02
82 130 0.71
83 11 0.06
84 39 0.21
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (81 bp):
TAAAAAACCAAGTTTATGAAAAGGGTAGTTCAGATTTTGCTCAAGAACTGCAAAATGAACTCTGA
AATGATTAAACAATTA
Found at i:79908 original size:3 final size:3
Alignment explanation
Indices: 79900--79928 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
79890 ATAACCCAAA
79900 AAG AAG AAG AAG AAG AAG AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
79929 CAACCTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:83592 original size:89 final size:89
Alignment explanation
Indices: 83438--83615 Score: 320
Period size: 89 Copynumber: 2.0 Consensus size: 89
83428 CTCGATTTTG
* * *
83438 ATTTACAACTATCAATGGTCTGATATAAGAATAAGTGTCCAAAATGTAATGCCCTGAATTATGAG
1 ATTTACAACTATCAATGGTCTGATATAAGAAAAAGTGTCCAAAATGTAATACCCTAAATTATGAG
83503 TTTTAGTTTCAGATTGACTCGAGA
66 TTTTAGTTTCAGATTGACTCGAGA
*
83527 ATTTACAACTATCAATGGTCTGATATAAGAAAAAGTGTCCAAAATGTAATACCCTAAATTCTGAG
1 ATTTACAACTATCAATGGTCTGATATAAGAAAAAGTGTCCAAAATGTAATACCCTAAATTATGAG
83592 TTTTAGTTTCAGATTGACTCGAGA
66 TTTTAGTTTCAGATTGACTCGAGA
83616 GGTATGTGGA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (89 bp):
ATTTACAACTATCAATGGTCTGATATAAGAAAAAGTGTCCAAAATGTAATACCCTAAATTATGAG
TTTTAGTTTCAGATTGACTCGAGA
Found at i:84354 original size:96 final size:96
Alignment explanation
Indices: 84190--84389 Score: 391
Period size: 96 Copynumber: 2.1 Consensus size: 96
84180 TATTTTTAAT
*
84190 CATTTGTGATGTTATAGCTTTCATAATCATGATGGTTTGGTGAGATTTGAGTGTTTGAACATGTT
1 CATTTTTGATGTTATAGCTTTCATAATCATGATGGTTTGGTGAGATTTGAGTGTTTGAACATGTT
84255 TGGGTTCTTGCTTGATTTATGCCCTAAATGA
66 TGGGTTCTTGCTTGATTTATGCCCTAAATGA
84286 CATTTTTGATGTTATAGCTTTCATAATCATGATGGTTTGGTGAGATTTGAGTGTTTGAACATGTT
1 CATTTTTGATGTTATAGCTTTCATAATCATGATGGTTTGGTGAGATTTGAGTGTTTGAACATGTT
84351 TGGGTTCTTGCTTGATTTATGCCCTAAATGA
66 TGGGTTCTTGCTTGATTTATGCCCTAAATGA
84382 CATTTTTG
1 CATTTTTG
84390 TTGTAAAGCT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 103 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.45
Consensus pattern (96 bp):
CATTTTTGATGTTATAGCTTTCATAATCATGATGGTTTGGTGAGATTTGAGTGTTTGAACATGTT
TGGGTTCTTGCTTGATTTATGCCCTAAATGA
Found at i:87396 original size:14 final size:14
Alignment explanation
Indices: 87377--87404 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
87367 GACGAAACTG
87377 AAAACAAAAAAAAA
1 AAAACAAAAAAAAA
87391 AAAACAAAAAAAAA
1 AAAACAAAAAAAAA
87405 TTGATTCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAAAAA
Found at i:88248 original size:21 final size:22
Alignment explanation
Indices: 88222--88273 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
88212 ATCCCTCTAT
* *
88222 ATATTTTTTTTCAAT-TAAATC
1 ATATTTTTTTTCAATAAAAATA
* *
88243 ATATTTTTATTGAATAAAAATA
1 ATATTTTTTTTCAATAAAAATA
88265 ATATTTTTT
1 ATATTTTTT
88274 ATTATTTCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTTTTTTTCAATAAAAATA
Found at i:94199 original size:17 final size:17
Alignment explanation
Indices: 94177--94212 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
94167 GTTGAAAATG
94177 AAAAAAAAAAAAACAAA
1 AAAAAAAAAAAAACAAA
* *
94194 AAAAAAAGAAAAAGAAA
1 AAAAAAAAAAAAACAAA
94211 AA
1 AA
94213 GGAGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.92, C:0.03, G:0.06, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAACAAA
Found at i:94573 original size:26 final size:27
Alignment explanation
Indices: 94521--94572 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
94511 TGTAATCGGT
*
94521 TTCGGTTTGCAAAAAACCGGTTTTTTA
1 TTCGGTTTGAAAAAAACCGGTTTTTTA
*
94548 TTCGGTTTGAAAAAAATCGGTTTTT
1 TTCGGTTTGAAAAAAACCGGTTTTT
94573 AATCCGGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (27 bp):
TTCGGTTTGAAAAAAACCGGTTTTTTA
Found at i:94580 original size:27 final size:27
Alignment explanation
Indices: 94523--94592 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
94513 TAATCGGTTT
* * * *
94523 CGGTTTGCAAAAAACCGGTTTTTTATT
1 CGGTTTGAAAAAAATCGGTTTTTAATC
94550 CGGTTTGAAAAAAATCGGTTTTTAATC
1 CGGTTTGAAAAAAATCGGTTTTTAATC
94577 CGG--T-AAAAAAATCGGT
1 CGGTTTGAAAAAAATCGGT
94593 CGTTCAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
24 12 0.31
25 1 0.03
27 26 0.67
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (27 bp):
CGGTTTGAAAAAAATCGGTTTTTAATC
Found at i:95526 original size:16 final size:17
Alignment explanation
Indices: 95494--95529 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
95484 TAAATCACTA
*
95494 TTTTAGGTATTCAAAAT
1 TTTTAGATATTCAAAAT
95511 TTTTAGATATTC-AAAT
1 TTTTAGATATTCAAAAT
95527 TTT
1 TTT
95530 GGGATTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTTAGATATTCAAAAT
Found at i:108694 original size:72 final size:71
Alignment explanation
Indices: 108562--108780 Score: 298
Period size: 71 Copynumber: 3.1 Consensus size: 71
108552 CTTCCAACTC
* *
108562 ATTTTGCCCAATATCTAGCGTTCCTAAA-TTTTCAACTGCCCAAAACTTGGAAGAAGAGGACCAT
1 ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGG-AGAAGAGGACCAT
108626 TTAATTG
65 TTAATTG
* * *
108633 ATTTTGCCAAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAGACTTGGAGGAAAAGGACCAT
1 ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGA-GAAGAGGACCAT
108698 TTAATTG
65 TTAATTG
** * * * *
108705 ATTTTGCCCAATATCTAGAGTTTCT-AATTTGCCAATTTCCCAAAATTTGGAGACAGAGTACCAT
1 ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGAGA-AGAGGACCAT
108769 TTAATTG
65 TTAATTG
108776 ATTTT
1 ATTTT
108781 CTGAAACATC
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
70 2 0.02
71 66 0.50
72 63 0.48
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (71 bp):
ATTTTGCCCAATATCTAGAGTTTCTAAATTTTTCAACTGCCCAAAACTTGGAGAAGAGGACCATT
TAATTG
Done.